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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.7

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2020-03-14, 14:15 based on data in: /scratch/ccrsf_scratch/scratch/Analysis/200313_A00430_0178_AHJJKWDRXX/JingWu_CS026381_44RNA_021320


        General Statistics

        Showing 220/220 rows and 10/12 columns.
        Sample Name% Alignable% rRNA% mRNA% Dups% AlignedM Aligned% Trimmed% GCLengthM Seqs
        10_923_L_R4
        95.5%
        0.0%
        91.4%
        24.8%
        91.7%
        21.5
        10_923_L_R4_R1
        48%
        151 bp
        23.4
        10_923_L_R4_R2
        7.2%
        48%
        151 bp
        23.4
        10_923_L_R4_trimmed_R1
        48%
        140 bp
        23.4
        10_923_L_R4_trimmed_R2
        48%
        140 bp
        23.4
        11_923_O_R4
        95.6%
        0.0%
        92.2%
        26.6%
        91.6%
        19.2
        11_923_O_R4_R1
        48%
        151 bp
        20.9
        11_923_O_R4_R2
        7.6%
        48%
        151 bp
        20.9
        11_923_O_R4_trimmed_R1
        48%
        140 bp
        20.9
        11_923_O_R4_trimmed_R2
        48%
        140 bp
        20.9
        12_923_LO_R4
        96.1%
        0.0%
        91.8%
        22.9%
        92.2%
        17.6
        12_923_LO_R4_R1
        49%
        151 bp
        19.2
        12_923_LO_R4_R2
        7.9%
        49%
        151 bp
        19.2
        12_923_LO_R4_trimmed_R1
        49%
        139 bp
        19.1
        12_923_LO_R4_trimmed_R2
        48%
        139 bp
        19.1
        13_827_C_RP1
        96.0%
        0.0%
        92.7%
        26.7%
        92.4%
        20.1
        13_827_C_RP1_R1
        48%
        151 bp
        21.8
        13_827_C_RP1_R2
        7.2%
        49%
        151 bp
        21.8
        13_827_C_RP1_trimmed_R1
        48%
        140 bp
        21.8
        13_827_C_RP1_trimmed_R2
        48%
        140 bp
        21.8
        14_827_L_RP1
        93.3%
        0.0%
        92.2%
        25.1%
        90.1%
        16.3
        14_827_L_RP1_R1
        49%
        151 bp
        18.1
        14_827_L_RP1_R2
        6.8%
        49%
        151 bp
        18.1
        14_827_L_RP1_trimmed_R1
        48%
        141 bp
        18.1
        14_827_L_RP1_trimmed_R2
        48%
        141 bp
        18.1
        15_827_O_RP1
        95.4%
        0.0%
        92.1%
        25.4%
        91.9%
        18.0
        15_827_O_RP1_R1
        48%
        151 bp
        19.5
        15_827_O_RP1_R2
        7.5%
        48%
        151 bp
        19.5
        15_827_O_RP1_trimmed_R1
        48%
        140 bp
        19.5
        15_827_O_RP1_trimmed_R2
        48%
        140 bp
        19.5
        16_827_LO_RP1
        94.7%
        0.0%
        92.2%
        26.6%
        91.2%
        18.3
        16_827_LO_RP1_R1
        49%
        151 bp
        20.1
        16_827_LO_RP1_R2
        8.9%
        48%
        151 bp
        20.1
        16_827_LO_RP1_trimmed_R1
        48%
        138 bp
        20.0
        16_827_LO_RP1_trimmed_R2
        48%
        138 bp
        20.0
        17_827_C_RP2
        95.9%
        0.0%
        89.7%
        24.5%
        92.3%
        21.0
        17_827_C_RP2_R1
        48%
        151 bp
        22.8
        17_827_C_RP2_R2
        7.6%
        48%
        151 bp
        22.8
        17_827_C_RP2_trimmed_R1
        48%
        140 bp
        22.8
        17_827_C_RP2_trimmed_R2
        48%
        140 bp
        22.8
        18_827_L_RP2
        95.6%
        0.0%
        90.7%
        25.5%
        91.9%
        19.9
        18_827_L_RP2_R1
        48%
        151 bp
        21.7
        18_827_L_RP2_R2
        7.2%
        49%
        151 bp
        21.7
        18_827_L_RP2_trimmed_R1
        48%
        140 bp
        21.7
        18_827_L_RP2_trimmed_R2
        48%
        140 bp
        21.7
        19_827_O_RP2
        96.1%
        0.0%
        91.1%
        25.0%
        92.5%
        17.5
        19_827_O_RP2_R1
        48%
        151 bp
        19.0
        19_827_O_RP2_R2
        7.3%
        48%
        151 bp
        19.0
        19_827_O_RP2_trimmed_R1
        48%
        140 bp
        18.9
        19_827_O_RP2_trimmed_R2
        48%
        140 bp
        18.9
        1_923_C_RP2
        95.5%
        0.0%
        92.4%
        25.3%
        91.5%
        18.0
        1_923_C_RP2_R1
        48%
        151 bp
        19.7
        1_923_C_RP2_R2
        10.2%
        48%
        151 bp
        19.7
        1_923_C_RP2_trimmed_R1
        47%
        136 bp
        19.6
        1_923_C_RP2_trimmed_R2
        47%
        136 bp
        19.6
        20_827_LO_RP2
        94.2%
        0.0%
        92.3%
        25.5%
        90.7%
        21.4
        20_827_LO_RP2_R1
        49%
        151 bp
        23.6
        20_827_LO_RP2_R2
        7.5%
        49%
        151 bp
        23.6
        20_827_LO_RP2_trimmed_R1
        49%
        140 bp
        23.6
        20_827_LO_RP2_trimmed_R2
        49%
        140 bp
        23.6
        21_827_C_R3
        95.9%
        0.0%
        92.7%
        27.3%
        92.1%
        21.9
        21_827_C_R3_R1
        49%
        151 bp
        23.8
        21_827_C_R3_R2
        7.8%
        49%
        151 bp
        23.8
        21_827_C_R3_trimmed_R1
        48%
        139 bp
        23.8
        21_827_C_R3_trimmed_R2
        48%
        139 bp
        23.8
        22_827_L_R3
        95.7%
        0.0%
        92.5%
        25.8%
        91.8%
        21.8
        22_827_L_R3_R1
        49%
        151 bp
        23.8
        22_827_L_R3_R2
        8.6%
        49%
        151 bp
        23.8
        22_827_L_R3_trimmed_R1
        49%
        138 bp
        23.8
        22_827_L_R3_trimmed_R2
        49%
        138 bp
        23.8
        23_827_O_R3
        94.7%
        0.0%
        92.0%
        25.6%
        91.2%
        18.0
        23_827_O_R3_R1
        49%
        151 bp
        19.7
        23_827_O_R3_R2
        6.8%
        49%
        151 bp
        19.7
        23_827_O_R3_trimmed_R1
        49%
        141 bp
        19.7
        23_827_O_R3_trimmed_R2
        48%
        141 bp
        19.7
        24_827_LO_R3
        94.5%
        0.0%
        92.1%
        23.8%
        91.0%
        16.5
        24_827_LO_R3_R1
        49%
        151 bp
        18.1
        24_827_LO_R3_R2
        9.1%
        49%
        151 bp
        18.1
        24_827_LO_R3_trimmed_R1
        48%
        137 bp
        18.1
        24_827_LO_R3_trimmed_R2
        48%
        138 bp
        18.1
        25_417_C_RP1
        94.8%
        0.0%
        92.2%
        28.0%
        91.1%
        23.1
        25_417_C_RP1_R1
        48%
        151 bp
        25.4
        25_417_C_RP1_R2
        8.8%
        48%
        151 bp
        25.4
        25_417_C_RP1_trimmed_R1
        48%
        138 bp
        25.4
        25_417_C_RP1_trimmed_R2
        48%
        138 bp
        25.4
        26_417_L_RP1
        95.9%
        0.0%
        91.8%
        27.1%
        92.0%
        20.1
        26_417_L_RP1_R1
        49%
        151 bp
        21.9
        26_417_L_RP1_R2
        7.8%
        49%
        151 bp
        21.9
        26_417_L_RP1_trimmed_R1
        48%
        139 bp
        21.9
        26_417_L_RP1_trimmed_R2
        48%
        140 bp
        21.9
        27_417_O_RP1
        95.2%
        0.0%
        92.2%
        27.3%
        91.5%
        18.0
        27_417_O_RP1_R1
        48%
        151 bp
        19.7
        27_417_O_RP1_R2
        7.2%
        49%
        151 bp
        19.7
        27_417_O_RP1_trimmed_R1
        48%
        140 bp
        19.7
        27_417_O_RP1_trimmed_R2
        48%
        140 bp
        19.7
        28_417_LO_RP1
        95.7%
        0.0%
        92.2%
        26.3%
        91.9%
        21.9
        28_417_LO_RP1_R1
        49%
        151 bp
        23.9
        28_417_LO_RP1_R2
        6.8%
        49%
        151 bp
        23.9
        28_417_LO_RP1_trimmed_R1
        48%
        141 bp
        23.9
        28_417_LO_RP1_trimmed_R2
        48%
        141 bp
        23.9
        29_417_C_RP2
        93.7%
        0.0%
        91.2%
        26.7%
        90.2%
        19.4
        29_417_C_RP2_R1
        48%
        151 bp
        21.6
        29_417_C_RP2_R2
        7.2%
        48%
        151 bp
        21.6
        29_417_C_RP2_trimmed_R1
        48%
        140 bp
        21.5
        29_417_C_RP2_trimmed_R2
        48%
        141 bp
        21.5
        2_923_L_RP2
        95.6%
        0.0%
        91.0%
        23.8%
        92.0%
        21.0
        2_923_L_RP2_R1
        48%
        151 bp
        22.8
        2_923_L_RP2_R2
        7.3%
        48%
        151 bp
        22.8
        2_923_L_RP2_trimmed_R1
        48%
        140 bp
        22.8
        2_923_L_RP2_trimmed_R2
        48%
        140 bp
        22.8
        30_417_L_RP2
        95.8%
        0.0%
        91.5%
        26.2%
        91.9%
        17.8
        30_417_L_RP2_R1
        48%
        151 bp
        19.4
        30_417_L_RP2_R2
        7.0%
        48%
        151 bp
        19.4
        30_417_L_RP2_trimmed_R1
        48%
        140 bp
        19.4
        30_417_L_RP2_trimmed_R2
        48%
        141 bp
        19.4
        31_417_O_RP2
        95.1%
        0.0%
        91.8%
        27.3%
        91.4%
        20.5
        31_417_O_RP2_R1
        48%
        151 bp
        22.5
        31_417_O_RP2_R2
        8.0%
        48%
        151 bp
        22.5
        31_417_O_RP2_trimmed_R1
        48%
        139 bp
        22.5
        31_417_O_RP2_trimmed_R2
        48%
        139 bp
        22.5
        32_417_LO_RP2
        94.2%
        0.0%
        90.8%
        26.1%
        90.5%
        16.7
        32_417_LO_RP2_R1
        48%
        151 bp
        18.4
        32_417_LO_RP2_R2
        10.0%
        49%
        151 bp
        18.4
        32_417_LO_RP2_trimmed_R1
        48%
        136 bp
        18.4
        32_417_LO_RP2_trimmed_R2
        48%
        136 bp
        18.4
        33_417_C_R3
        94.8%
        0.0%
        91.9%
        27.0%
        91.1%
        20.6
        33_417_C_R3_R1
        47%
        151 bp
        22.7
        33_417_C_R3_R2
        7.5%
        47%
        151 bp
        22.7
        33_417_C_R3_trimmed_R1
        47%
        140 bp
        22.6
        33_417_C_R3_trimmed_R2
        47%
        140 bp
        22.6
        34_417_L_R3
        95.6%
        0.0%
        92.7%
        26.4%
        91.7%
        18.5
        34_417_L_R3_R1
        48%
        151 bp
        20.2
        34_417_L_R3_R2
        8.1%
        49%
        151 bp
        20.2
        34_417_L_R3_trimmed_R1
        48%
        139 bp
        20.2
        34_417_L_R3_trimmed_R2
        48%
        139 bp
        20.2
        35_417_O_R3
        95.6%
        0.0%
        92.0%
        27.7%
        91.6%
        20.4
        35_417_O_R3_R1
        48%
        151 bp
        22.3
        35_417_O_R3_R2
        7.0%
        48%
        151 bp
        22.3
        35_417_O_R3_trimmed_R1
        48%
        141 bp
        22.3
        35_417_O_R3_trimmed_R2
        48%
        141 bp
        22.3
        36_417_LO_R3
        94.2%
        0.0%
        92.5%
        26.6%
        90.3%
        17.7
        36_417_LO_R3_R1
        49%
        151 bp
        19.6
        36_417_LO_R3_R2
        8.8%
        49%
        151 bp
        19.6
        36_417_LO_R3_trimmed_R1
        49%
        138 bp
        19.6
        36_417_LO_R3_trimmed_R2
        48%
        138 bp
        19.6
        37_602_C_RP1
        94.2%
        0.0%
        90.5%
        28.0%
        90.5%
        17.8
        37_602_C_RP1_R1
        48%
        151 bp
        19.7
        37_602_C_RP1_R2
        7.2%
        48%
        151 bp
        19.7
        37_602_C_RP1_trimmed_R1
        48%
        140 bp
        19.7
        37_602_C_RP1_trimmed_R2
        48%
        140 bp
        19.7
        38_602_L_RP1
        94.4%
        0.0%
        89.6%
        26.8%
        90.5%
        18.2
        38_602_L_RP1_R1
        48%
        151 bp
        20.1
        38_602_L_RP1_R2
        8.3%
        48%
        151 bp
        20.1
        38_602_L_RP1_trimmed_R1
        48%
        139 bp
        20.1
        38_602_L_RP1_trimmed_R2
        48%
        139 bp
        20.1
        39_602_O_RP1
        95.3%
        0.0%
        89.5%
        27.6%
        91.4%
        20.3
        39_602_O_RP1_R1
        48%
        151 bp
        22.2
        39_602_O_RP1_R2
        8.8%
        48%
        151 bp
        22.2
        39_602_O_RP1_trimmed_R1
        48%
        138 bp
        22.2
        39_602_O_RP1_trimmed_R2
        48%
        138 bp
        22.2
        3_923_O_RP2
        95.8%
        0.0%
        91.4%
        24.7%
        91.9%
        19.0
        3_923_O_RP2_R1
        48%
        151 bp
        20.7
        3_923_O_RP2_R2
        7.5%
        49%
        151 bp
        20.7
        3_923_O_RP2_trimmed_R1
        48%
        140 bp
        20.6
        3_923_O_RP2_trimmed_R2
        48%
        140 bp
        20.6
        40_602_LO_RP1
        94.5%
        0.0%
        89.8%
        27.5%
        90.5%
        19.9
        40_602_LO_RP1_R1
        48%
        151 bp
        22.1
        40_602_LO_RP1_R2
        11.2%
        49%
        151 bp
        22.1
        40_602_LO_RP1_trimmed_R1
        48%
        134 bp
        22.0
        40_602_LO_RP1_trimmed_R2
        48%
        134 bp
        22.0
        41_602_C_RP2
        95.5%
        0.0%
        89.5%
        26.4%
        91.4%
        18.2
        41_602_C_RP2_R1
        47%
        151 bp
        19.9
        41_602_C_RP2_R2
        9.0%
        47%
        151 bp
        19.9
        41_602_C_RP2_trimmed_R1
        47%
        137 bp
        19.9
        41_602_C_RP2_trimmed_R2
        47%
        138 bp
        19.9
        42_602_L_RP2
        95.9%
        0.0%
        89.6%
        25.7%
        91.9%
        19.6
        42_602_L_RP2_R1
        48%
        151 bp
        21.3
        42_602_L_RP2_R2
        7.9%
        49%
        151 bp
        21.3
        42_602_L_RP2_trimmed_R1
        48%
        139 bp
        21.3
        42_602_L_RP2_trimmed_R2
        48%
        139 bp
        21.3
        43_602_O_RP2
        94.6%
        0.0%
        89.7%
        26.2%
        90.8%
        17.6
        43_602_O_RP2_R1
        48%
        151 bp
        19.4
        43_602_O_RP2_R2
        8.3%
        48%
        151 bp
        19.4
        43_602_O_RP2_trimmed_R1
        48%
        138 bp
        19.4
        43_602_O_RP2_trimmed_R2
        47%
        139 bp
        19.4
        44_602_LO_RP2
        95.1%
        0.0%
        89.4%
        25.5%
        91.3%
        18.8
        44_602_LO_RP2_R1
        48%
        151 bp
        20.6
        44_602_LO_RP2_R2
        7.5%
        48%
        151 bp
        20.6
        44_602_LO_RP2_trimmed_R1
        47%
        140 bp
        20.6
        44_602_LO_RP2_trimmed_R2
        47%
        140 bp
        20.6
        4_923_LO_RP2
        94.8%
        0.0%
        91.1%
        24.1%
        91.1%
        19.6
        4_923_LO_RP2_R1
        49%
        151 bp
        21.6
        4_923_LO_RP2_R2
        7.3%
        48%
        151 bp
        21.6
        4_923_LO_RP2_trimmed_R1
        48%
        140 bp
        21.5
        4_923_LO_RP2_trimmed_R2
        48%
        140 bp
        21.5
        5_923_C_R3
        94.8%
        0.0%
        91.3%
        25.6%
        91.1%
        23.0
        5_923_C_R3_R1
        49%
        151 bp
        25.3
        5_923_C_R3_R2
        8.1%
        49%
        151 bp
        25.3
        5_923_C_R3_trimmed_R1
        48%
        139 bp
        25.2
        5_923_C_R3_trimmed_R2
        48%
        139 bp
        25.2
        6_923_L_R3
        94.5%
        0.0%
        91.4%
        22.9%
        90.8%
        15.4
        6_923_L_R3_R1
        49%
        151 bp
        17.0
        6_923_L_R3_R2
        7.6%
        49%
        151 bp
        17.0
        6_923_L_R3_trimmed_R1
        49%
        140 bp
        17.0
        6_923_L_R3_trimmed_R2
        49%
        140 bp
        17.0
        7_923_O_R3
        94.6%
        0.0%
        91.6%
        23.1%
        90.9%
        15.5
        7_923_O_R3_R1
        49%
        151 bp
        17.0
        7_923_O_R3_R2
        7.7%
        49%
        151 bp
        17.0
        7_923_O_R3_trimmed_R1
        49%
        139 bp
        17.0
        7_923_O_R3_trimmed_R2
        49%
        140 bp
        17.0
        8_923_LO_R3
        94.8%
        0.0%
        91.1%
        25.0%
        91.2%
        21.3
        8_923_LO_R3_R1
        48%
        151 bp
        23.4
        8_923_LO_R3_R2
        8.5%
        48%
        151 bp
        23.4
        8_923_LO_R3_trimmed_R1
        48%
        138 bp
        23.3
        8_923_LO_R3_trimmed_R2
        48%
        138 bp
        23.3
        9_923_C_R4
        94.8%
        0.0%
        91.6%
        24.7%
        91.0%
        20.6
        9_923_C_R4_R1
        48%
        151 bp
        22.7
        9_923_C_R4_R2
        8.8%
        48%
        151 bp
        22.7
        9_923_C_R4_trimmed_R1
        48%
        138 bp
        22.6
        9_923_C_R4_trimmed_R2
        47%
        138 bp
        22.6

        Rsem

        Rsem RSEM (RNA-Seq by Expectation-Maximization) is a software package forestimating gene and isoform expression levels from RNA-Seq data.

        Mapped Reads

        A breakdown of how all reads were aligned for each sample.

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        Multimapping rates

        A frequency histogram showing how many reads were aligned to n reference regions.

        In an ideal world, every sequence reads would align uniquely to a single location in the reference. However, due to factors such as repeititve sequences, short reads and sequencing errors, reads can be align to the reference 0, 1 or more times. This plot shows the frequency of each factor of multimapping. Good samples should have the majority of reads aligning once.

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        RSeQC

        RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

        Read Distribution

        Read Distribution calculates how mapped reads are distributed over genome features.

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        Inner Distance

        Inner Distance calculates the inner distance (or insert size) between two paired RNA reads. Note that this can be negative if fragments overlap.

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        Read GC Content

        read_GC calculates a histogram of read GC content.

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        Infer experiment

        Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

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        Picard

        Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

        Mark Duplicates

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        RnaSeqMetrics Assignment

        Number of bases in primary alignments that align to regions in the reference genome.

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        RnaSeqMetrics Strand Mapping

        Number of aligned reads that map to the correct strand.

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        Gene Coverage

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        STAR

        STAR is an ultrafast universal RNA-seq aligner.

        Alignment Scores

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        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        This plot shows the number of reads with certain lengths of adapter trimmed. Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length. See the cutadapt documentation for more information on how these numbers are generated.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQ Screen

        FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

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        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        176 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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